feat(report): keep dependency findings from distinct manifests separate in dedupe

strix/report/dedupe.py

@@ -183,6 +183,24 @@ def _dependency_identity(report: dict[str, Any]) -> tuple[str, str, str] | None:
     return cve, ecosystem, package_name
 
 
+def _manifest_path(report: dict[str, Any]) -> str:
+    metadata = report.get("dependency_metadata")
+    if not isinstance(metadata, dict):
+        return ""
+    return str(metadata.get("manifest_path") or "").strip()
+
+
+def _distinct_manifest_paths(candidate: dict[str, Any], report: dict[str, Any]) -> bool:
+    """Same CVE/package observed in two different manifests is two findings.
+
+    Only applies when both sides carry a manifest_path; a missing path keeps
+    the legacy CVE/package/ecosystem identity.
+    """
+    candidate_path = _manifest_path(candidate)
+    report_path = _manifest_path(report)
+    return bool(candidate_path and report_path and candidate_path != report_path)
+
+
 def _report_cve(report: dict[str, Any]) -> str:
     return str(report.get("cve") or "").strip().upper()
 
@@ -228,6 +246,8 @@ def _check_dependency_duplicate(
             report_cve, report_ecosystem, report_package_name = report_identity
             if (report_cve, report_package_name) != (cve, package_name):
                 continue
+            if _distinct_manifest_paths(candidate, report):
+                continue
             if report_ecosystem == ecosystem:
                 return {
                     "is_duplicate": True,

strix/skills/custom/dependency_cve_scanning.md

@@ -77,8 +77,10 @@ For each entry under `.Results[].Vulnerabilities[]` in `trivy-sca.json`, collect
 - `CVSS` — the published advisory base score
 - `PrimaryURL` / references — to verify the advisory
 
-Deduplicate by `(CVE, PkgName, InstalledVersion)`. File one
-`create_dependency_report` per CVE — do not batch multiple CVEs into one report.
+Deduplicate by `(CVE, PkgName, Target)` — the same CVE/package observed in two
+different manifests (e.g. two workspaces of a monorepo) is two findings, one
+per manifest. File one `create_dependency_report` per CVE — do not batch
+multiple CVEs into one report.
 
 ### Attribute transitive CVEs to the direct dependency
 

tests/test_reporting_fields.py

@@ -653,6 +653,72 @@ async def test_dependency_dedupe_rejects_same_cve_package_identity() -> None:
     assert result["confidence"] == 1.0
 
 
+async def test_dependency_dedupe_keeps_findings_from_distinct_manifests() -> None:
+    existing = [
+        {
+            "id": "vuln-0001",
+            "title": "CVE-2024-0001 in sample",
+            "cve": "CVE-2024-0001",
+            "dependency_metadata": {
+                "package_name": "sample",
+                "installed_version": "1.0.0",
+                "package_ecosystem": "npm",
+                "manifest_path": "services/api/package-lock.json",
+            },
+        }
+    ]
+    candidate = {
+        "title": "CVE-2024-0001 in sample (web)",
+        "description": "Same advisory observed in a second workspace.",
+        "target": "repo/package.json",
+        "cve": "CVE-2024-0001",
+        "dependency_metadata": {
+            "package_name": "sample",
+            "installed_version": "1.0.0",
+            "package_ecosystem": "npm",
+            "manifest_path": "services/web/package-lock.json",
+        },
+    }
+
+    result = await check_duplicate(candidate, existing)
+
+    assert result["is_duplicate"] is False
+    assert result["confidence"] == 1.0
+
+
+async def test_dependency_dedupe_rejects_same_manifest_identity() -> None:
+    existing = [
+        {
+            "id": "vuln-0001",
+            "title": "CVE-2024-0001 in sample",
+            "cve": "CVE-2024-0001",
+            "dependency_metadata": {
+                "package_name": "sample",
+                "installed_version": "1.0.0",
+                "package_ecosystem": "npm",
+                "manifest_path": "services/api/package-lock.json",
+            },
+        }
+    ]
+    candidate = {
+        "title": "CVE-2024-0001 in sample re-reported",
+        "description": "Same advisory, same manifest.",
+        "target": "repo/package.json",
+        "cve": "CVE-2024-0001",
+        "dependency_metadata": {
+            "package_name": "sample",
+            "installed_version": "1.0.0",
+            "package_ecosystem": "npm",
+            "manifest_path": "services/api/package-lock.json",
+        },
+    }
+
+    result = await check_duplicate(candidate, existing)
+
+    assert result["is_duplicate"] is True
+    assert result["duplicate_id"] == "vuln-0001"
+
+
 async def test_dependency_dedupe_detects_legacy_same_cve_package() -> None:
     existing = [
         {